MolNFT v1 · #24903 · protein
Structure of E. COLI cyclophilin B K163T mutant bound to succinyl-ala- pro-ala-P-nitroanilide
1V9T: “Structure of E. COLI cyclophilin B K163T mutant bound to succinyl-ala- pro-ala-P-nitroanilide”. X-ray diffraction, 1 ligand (NIT), 2 pockets (best druggability 0.35). MolNFT v1 #24903 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1V9T
- Type
- protein
- Length
- 335 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclophilin B; (SIN)APA(NIT)
- EC
- 5.2.1.8
- UniProt
- P20752
- Ligands
- NIT
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclophilin B (EC 5.2.1.8) | protein | 166 | 16% helix, 35% strand | P20752 |
| C | (SIN)APA(NIT) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.35 | 0.76 | 18 | empty |
| 2 | 76 | 0.33 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 221 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 135 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 1V9T · Structure of E. coli cyclophilin B K163T mutant bound to… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P20752
- Elsewhere: RCSB PDB 1V9T · PDBe 1V9T · UniProt P20752
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